ColonyArea: an ImageJ plugin to automatically quantify colony formation in clonogenic assays.

The clonogenic or colony formation assay is a widely used method to study the number and size of cancer cell colonies that remain after irradiation or cytotoxic agent administration and serves as a measure for the anti-proliferative effect of these treatments. Alternatively, this assay is used to qu...

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Autores principales:	Camilo Guzmán, Manish Bagga, Amanpreet Kaur, Jukka Westermarck, Daniel Abankwa
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/87120b53182640f180664ed7d7d5b790
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spelling	oai:doaj.org-article:87120b53182640f180664ed7d7d5b7902021-11-18T08:27:18ZColonyArea: an ImageJ plugin to automatically quantify colony formation in clonogenic assays.1932-620310.1371/journal.pone.0092444https://doaj.org/article/87120b53182640f180664ed7d7d5b7902014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24647355/?tool=EBIhttps://doaj.org/toc/1932-6203The clonogenic or colony formation assay is a widely used method to study the number and size of cancer cell colonies that remain after irradiation or cytotoxic agent administration and serves as a measure for the anti-proliferative effect of these treatments. Alternatively, this assay is used to quantitate the transforming potential of cancer associated genes and chemical agents. Therefore, there is a need for a simplified and standardized analysis of colony formation assays for both routine laboratory use and for parallelized automated analysis. Here we describe the freely available ImageJ-plugin "ColonyArea", which is optimized for rapid and quantitative analysis of focus formation assays conducted in 6- to 24-well dishes. ColonyArea processes image data of multi-well dishes, by separating, concentrically cropping and background correcting well images individually, before colony formation is quantitated. Instead of counting the number of colonies, ColonyArea determines the percentage of area covered by crystal violet stained cell colonies, also taking the intensity of the staining and therefore cell density into account. We demonstrate that these parameters alone or in combination allow for robust quantification of IC50 values of the cytotoxic effect of two staurosporines, UCN-01 and staurosporine (STS) on human glioblastoma cells (T98G). The relation between the potencies of the two compounds compared very well with that obtained from an absorbance based method to quantify colony growth and to published data. The ColonyArea ImageJ plugin provides a simple and efficient analysis routine to quantitate assay data of one of the most commonly used cellular assays. The bundle is freely available for download as supporting information. We expect that ColonyArea will be of broad utility for cancer biologists, as well as clinical radiation scientists.Camilo GuzmánManish BaggaAmanpreet KaurJukka WestermarckDaniel AbankwaPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 3, p e92444 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Camilo Guzmán Manish Bagga Amanpreet Kaur Jukka Westermarck Daniel Abankwa ColonyArea: an ImageJ plugin to automatically quantify colony formation in clonogenic assays.
description	The clonogenic or colony formation assay is a widely used method to study the number and size of cancer cell colonies that remain after irradiation or cytotoxic agent administration and serves as a measure for the anti-proliferative effect of these treatments. Alternatively, this assay is used to quantitate the transforming potential of cancer associated genes and chemical agents. Therefore, there is a need for a simplified and standardized analysis of colony formation assays for both routine laboratory use and for parallelized automated analysis. Here we describe the freely available ImageJ-plugin "ColonyArea", which is optimized for rapid and quantitative analysis of focus formation assays conducted in 6- to 24-well dishes. ColonyArea processes image data of multi-well dishes, by separating, concentrically cropping and background correcting well images individually, before colony formation is quantitated. Instead of counting the number of colonies, ColonyArea determines the percentage of area covered by crystal violet stained cell colonies, also taking the intensity of the staining and therefore cell density into account. We demonstrate that these parameters alone or in combination allow for robust quantification of IC50 values of the cytotoxic effect of two staurosporines, UCN-01 and staurosporine (STS) on human glioblastoma cells (T98G). The relation between the potencies of the two compounds compared very well with that obtained from an absorbance based method to quantify colony growth and to published data. The ColonyArea ImageJ plugin provides a simple and efficient analysis routine to quantitate assay data of one of the most commonly used cellular assays. The bundle is freely available for download as supporting information. We expect that ColonyArea will be of broad utility for cancer biologists, as well as clinical radiation scientists.
format	article
author	Camilo Guzmán Manish Bagga Amanpreet Kaur Jukka Westermarck Daniel Abankwa
author_facet	Camilo Guzmán Manish Bagga Amanpreet Kaur Jukka Westermarck Daniel Abankwa
author_sort	Camilo Guzmán
title	ColonyArea: an ImageJ plugin to automatically quantify colony formation in clonogenic assays.
title_short	ColonyArea: an ImageJ plugin to automatically quantify colony formation in clonogenic assays.
title_full	ColonyArea: an ImageJ plugin to automatically quantify colony formation in clonogenic assays.
title_fullStr	ColonyArea: an ImageJ plugin to automatically quantify colony formation in clonogenic assays.
title_full_unstemmed	ColonyArea: an ImageJ plugin to automatically quantify colony formation in clonogenic assays.
title_sort	colonyarea: an imagej plugin to automatically quantify colony formation in clonogenic assays.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/87120b53182640f180664ed7d7d5b790
work_keys_str_mv	AT camiloguzman colonyareaanimagejplugintoautomaticallyquantifycolonyformationinclonogenicassays AT manishbagga colonyareaanimagejplugintoautomaticallyquantifycolonyformationinclonogenicassays AT amanpreetkaur colonyareaanimagejplugintoautomaticallyquantifycolonyformationinclonogenicassays AT jukkawestermarck colonyareaanimagejplugintoautomaticallyquantifycolonyformationinclonogenicassays AT danielabankwa colonyareaanimagejplugintoautomaticallyquantifycolonyformationinclonogenicassays
_version_	1718421752633098240

ColonyArea: an ImageJ plugin to automatically quantify colony formation in clonogenic assays.

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